Bibliothek

Notizen: Langevin Monte Carlo dynamics and equilibrium properties of the multicopy sampling approximation in the modeling of ligand–protein complexes are studied. A perturbation form is derived based on the normal mode analysis, and can be used as a quantitative means to estimate the approximation prior to running a multicopy simulation. The multicopy dynamics is shown to induce an average dynamics of the protein and all the ligand copies, resulting in a well-defined equilibrium with uniform temperature. The induced average dynamics and the equilibrium represent the desired physics of the multicopy approximation, and are extended to include heterogeneous ligand copies. Such an extension presents a natural way to incorporate biologically important information on evolution into energy-based molecular modeling of homologous proteins.

Notizen: In this work, we test a hypothesized form for the stationary solution Ps(X,Y) of the stochastic master equation for a reacting chemical system with two reactive intermediates X and Y, and multiple steady states. Thermodynamic analyses and the exact results for nonautocatalytic or equilibrating systems suggest an approximation of the form Pas(X,Y)=N exp(−φ/kT), where the function φ is a line integral of a differential "excess'' work Fφ, which depends on species-specific affinities. The differential Fφ is inexact. In a preceding paper, we have given an analytic argument for the use of the deterministic kinetic trajectory, connecting (X,Y) to the steady state (Xs,Ys) as the path of integration for Fφ. Here, we show that use of the deterministic trajectories leads to a potential φdet which is continuous across the separatrix between the domains of attraction of the two stable steady states in the model studied.We compare the approximate form of Ps(X,Y) thus generated with numerical solutions of the time-dependent master equation in the limit of attainment of a stationary distribution. Because the time required for convergence to the stationary distribution scales as eN with the particle number N in cases with two stable steady states, the numerical work is limited to systems with O(10–100) X and Y particles. System size affects the accuracy of the approximation. To isolate system-size effects, we compare numerical solutions and the corresponding approximations to Ps(X) for two single-intermediate master equations, since the approximation becomes exact in the limit of large particle number for such equations. Based on these comparisons, for the systems with two intermediates, the agreement between the approximation and the numerical solutions is reasonable. The agreement improves as the number of particles increases in those test cases where it has thus far been possible to vary the system size over an order of magnitude. The results obtained by integrating along deterministic trajectories are better than those from straight-line or line-segment paths. The numerical work on small, single-variable systems with two stable steady states leads to two new observations: (i) the relative heights of the steady state peaks in the exact stationary distribution may invert as the system size increases and (ii) an approximation used commonly for particle counting may give results inconsistent with the exact stationary distribution when the particle number is small, while an alternative approximation improves the agreement.

Notizen: The deterministic kinetics of chemical reactions is compared with a stochastic description for the cubic Schlögl model with a single stable steady state, which has a nonlinear reaction mechanism. We solve numerically the birth-death master equation for this system for various numbers of particles (N=20–160). For small systems with tens of particles the deviation of the first moment of the stochastic distribution from the deterministic temporal variation of concentration can be substantial in the initial relaxation towards a stationary state. The relaxation of the master equation is faster than that of the deterministic equation. The maximum deviation in trajectories decreases as the parameters in the kinetic model are altered towards a linear mechanism. The maximum deviation differs from N1/2 as N decreases, but approaches N1/2 as N increases. Deviations from deterministic temporal evolution due to fluctuations depend on the extent of nonlinearity of the reaction. The variance of a stationary distribution of the master equation is shown to be significantly larger than the average for a nonlinear system.

Notizen: Based on the integration research, one multi-dimension integrated mode of CAPP and PDM was proposed including the integration of knowledge store dimension, knowledge transfer dimension and knowledge application dimension. In the integration of knowledge application dimension, an innovated integration method named key control function module was proposed. In knowledge transfer dimension integration, a recursive model of task and workflow between CAPP and PDM was made. In knowledge store dimension integration, the federal database and the virtualfederal database was described

Notizen: Bone grafts have been used to fill bone defects caused by disease or trauma. The amount ofautografts is limited and allogenic bone grafts may transmit diseases and cause immune responses.Numerous materials have been proposed and used as scaffolds for bone tissue reconstruction. In thisstudy, we tested nanophase PLGA/HA composite with mesenchymal stem cells in vitro to examineits biological response and cellular activity. The nanophase composite was compared toconventional polystyrene on cytocompatibility by cell attachment, proliferation, alkalinephosphotase activity test and scanning electron microscopy (SEM) analysis. The resultsdemonstrated that human mesenchymal cells showed more cell attachment and higher cellproliferation rate when growing on nanophase PLGA/HA composite than those growing onpolystyrene alone. And the composite also promoted MSC cells differentiate to osteoblast cells ascompared with control. It was suggested that the combination of bone marrow mesenchymal cellswith artificial materials or differentiation factors may enhance bone formation and regeneration,nanophase PLGA/HA composite might therefore be a promising scaffold material for bone tissuesubstitute in clinical application

Notizen: The measuring system was developed based on a reconstructed atomic force microscope(AFM) combined with the precision rotating air-bearing and assistant transform shaft. By thissystem the experiment was carried out according to the principle of three orthogonal orientationstowards a micro sphere about 0.46 mm in diameter, and nine one-dimensional traces around thesphere were obtained. Analyses on roundness and sphericity are carried out from the measureddata.The results show that the maximal roundness is 0.3895 μm, and the sphericity error is 0.3880μm.These evaluations are significant references to evaluate its fabrication accuracy or to reform itsmachining processes

Notizen: The existence of residual stresses caused by the welding process is an important reason of cracking and distortion in welded metal structures that may affect the fatigue life and dimensional stability significantly. Heat treatment is one of the traditional methods to relieve the residual stresses. But it is often limited by the manufacturing condition and the size of the structures. In this paper a procedure called vibratory stress relief (VSR) is discussed. VSR is a process to reduce and re-distribute the internal residual stresses of welded structures by means of post-weld mechanical vibration. The effectiveness of VSR on the residual stresses of welded structures, including the drums of hoist machine and thick stainless steel plate are investigated. Parameters of VSR procedure are described in the paper. Residual stresses on weld bead are measured before and after VSR treatment by hole-drilling method and about 30%~50% reduction of residual stresses are observed. The results show that VSR process can reduce the residual stress both middle carbon steel (Q345) and stainless steel (304L) welded structures effectively